The purpose of this study was to determine the effect of flooding and high rainfall on water quality at selected points along the Vaal River, Wilge River and Vaal Dam that make up part of the Upper Vaal Catchment Area. Four study sites were selected, three along a section of the Vaal River that flows from Standerton (site S-ST_NEW) through Villiers (site C-VV) into the Vaal Dam ( C-VD21). The fourth site is on the Wilge River at Frankfort (C-WF) and joins with the Vaal River at site C-VD21 in the Vaal Dam. For each of these four sites seven water quality parameters, namely Chemical Oxygen Demand (COD), conductivity, chloride, fluoride, orthophosphate, sulphate and faecal coliforms where used to determine if there is a change in water quality during flooding and high rainfall in a six year period from 2005 to 2011. This period included the 2006 and 2011 floods and the 2009 high rainfall period. The results of this study demonstrated two types of changes that flooding and high rainfall can cause, either a dilution effect or a concentrating effect. Dilution is caused by low runoff of a particular pollutant/contaminant with an increase in water volume while the concentrating effect is due to a much increased runoff of a particular pollutant/contaminant. Results were not consistent. However general trends could be observed at specific sites. As a general rule, dilution occurred in the following parameters: conductivity; chloride, orthophosphate, COD and faecal coliforms. The remaining water quality parameters, namely fluoride and sulphate showed a general tendency to increase in concentration during flooding and high rainfall. The effect of floods on the quality of the water using the Vaal Dam Reservoir Forum (VDRS) water quality guidelines for sites C-VV, C-WF and C-VD21 and the Sewage Works Compliance to general standard for site S-ST_NEW was also studied. In general, flooding and high rainfall had very little effect in changing water quality, in that parameter levels were not altered significantly enough to cause a change in water quality. However, in some circumstances water quality was reduced. The statistical two-tailed one-sample t-test and p-value for the most part did not yield any significant difference in water quality during flooding and high rainfall and the sixyear average.